Nope... Boot mode and flashing/reading with the NefMoto Flasher are two separate things.
edit to clarify: You should be able to over-write your current flash with NefMoto, but you are unable to read it because your tuner has removed/disabled the code that allows reading. If they have gone to the effort to remove the code to read, they probably also went to the effort to move the map locations or obfuscate them, which means depending on your skillset, you may be better off just starting from a factory tune, and modifying the appropriate documented maps. This will also restore your ability to read-write over OBD.
I found myself in the same shoes as you, and am glad I decided to start fresh instead of build on the mistakes of the tuner.
My tuner is not in question here. That's an entirely separate discussion, actually. My concern is only with how to get my current tune off of my ECU, modify it to reallow flashing via OBD, and to delete out some emissions stuff while I'm in there.
Anyways, it sounds like powering up in boot mode and trying over OBD isn't enough, and that I'll have to get a full blown programmer and read directly from the EEPROM.
Thanks for your help.